1
|
Peng J, Liu W, Tang S, Zou S, Zhu Y, Cheng H, Wang Y, Streit WR, Chen Z, Zhou H. Identification and biochemical characterization of a novel GH113 β-mannanase from acid mine drainage metagenome. Biochem Eng J 2023. [DOI: 10.1016/j.bej.2023.108837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
|
2
|
Feng S, Qiu Y, Huang Z, Yin Y, Zhang H, Zhu D, Tong Y, Yang H. The adaptation mechanisms of Acidithiobacillus caldus CCTCC M 2018054 to extreme acid stress: Bioleaching performance, physiology, and transcriptomics. ENVIRONMENTAL RESEARCH 2021; 199:111341. [PMID: 34015291 DOI: 10.1016/j.envres.2021.111341] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 05/09/2023]
Abstract
To understand the acid-resistant mechanism of bioleaching microorganism Acidithiobacillus caldus CCTCC M 2018054, its physiology and metabolic changes at the transcriptional level under extreme acid stress were systemically studied. Scanning electron microscopy (SEM), Fourier transform infrared reflection (FTIR) and X-ray diffraction (XRD) showed that with an increase in acidity, the absorption peak of sulfur oxidation-related functional groups such as S-O decreased significantly, and a dense sulfur passivation film appeared on the surface of the ore. Confocal laser scanning microscopy (CLSM) revealed that coverage scale of extracellular polymeric substance (EPS) and biofilm fluctuated accordingly along with the increasing acid stress (pH-stat 1.5, 1.2 0.9 and 0.6) during the bioleaching process. In response to acid stress, the increased levels of intracellular glutamic acid, alanine, cysteine, and proline contributed to the maintenance of intracellular pH homeostasis via decarboxylation and alkaline neutralization. Higher unsaturated fatty acid content was closely related to membrane fluidity. Up to 490 and 447 differentially expressed genes (DEGs) were identified at pH 1.5 vs pH 1.2 and pH 1.2 vs pH 0.9, respectively, and 177 common DEGs were associated with two-component system (TCS) regulation, transporter regulation, energy metabolism, and stress response. The upregulation of kdpB helped cells defend against proton invasion, whereas the downregulation of cysB and cbl implied stronger oxidation of sulfur compounds. The transcriptional level of sqr, sor, and soxA was significantly increased and consolidated the energy supply needed for resisting acid stress. Furthermore, eight of the identified DEGs (sor, cbl, ompA, atpF, nuoH, nuoC, sqr, grxB) were verified as being related to the acid stress response process. This study contributes toward expanding the application of these acidophiles in industrial bioleaching.
Collapse
Affiliation(s)
- Shoushuai Feng
- Key Laboratory of Carbohydrate Chemistry and Biotechnology (Jiangnan University) Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yongkang Qiu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology (Jiangnan University) Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhuangzhuang Huang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology (Jiangnan University) Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yijun Yin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology (Jiangnan University) Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Hailing Zhang
- Department of Biological Engineering, College of Life Science, Yantai University, Shandong, 408100, China
| | - Deqiang Zhu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, 250353, China
| | - Yanjun Tong
- Key Laboratory of Carbohydrate Chemistry and Biotechnology (Jiangnan University) Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.
| | - Hailin Yang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology (Jiangnan University) Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, China.
| |
Collapse
|
3
|
Gottesman ME, Chudaev M, Mustaev A. Key features of magnesium that underpin its role as the major ion for electrophilic biocatalysis. FEBS J 2020; 287:5439-5463. [DOI: 10.1111/febs.15318] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 02/06/2020] [Accepted: 03/30/2020] [Indexed: 01/05/2023]
Affiliation(s)
- Max E. Gottesman
- Department of Microbiology & Immunology Columbia University Medical Center New York NY USA
| | - Maxim Chudaev
- Public Health Research Institute & Department of Microbiology and Molecular Genetics New Jersey Medical School Rutgers Biomedical and Health Sciences Newark NJ USA
| | - Arkady Mustaev
- Public Health Research Institute & Department of Microbiology and Molecular Genetics New Jersey Medical School Rutgers Biomedical and Health Sciences Newark NJ USA
| |
Collapse
|
4
|
Chen SH, Yu X. Human DNA ligase IV is able to use NAD+ as an alternative adenylation donor for DNA ends ligation. Nucleic Acids Res 2019; 47:1321-1334. [PMID: 30496552 PMCID: PMC6379666 DOI: 10.1093/nar/gky1202] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 11/09/2018] [Accepted: 11/15/2018] [Indexed: 12/29/2022] Open
Abstract
All the eukaryotic DNA ligases are known to use adenosine triphosphate (ATP) for DNA ligation. Here, we report that human DNA ligase IV, a key enzyme in DNA double-strand break (DSB) repair, is able to use NAD+ as a substrate for double-stranded DNA ligation. In the in vitro ligation assays, we show that the recombinant Ligase IV can use both ATP and NAD+ for DNA ligation. For NAD+-mediated ligation, the BRCA1 C-terminal (BRCT) domain of Ligase IV recognizes NAD+ and facilitates the adenylation of Ligase IV, the first step of ligation. Although XRCC4, the functional partner of Ligase IV, is not required for the NAD+-mediated adenylation, it regulates the transfer of AMP moiety from Ligase IV to the DNA end. Moreover, cancer-associated mutation in the BRCT domain of Ligase IV disrupts the interaction with NAD+, thus abolishes the NAD+-mediated adenylation of Ligase IV and DSB ligation. Disrupting the NAD+ recognition site in the BRCT domain impairs non-homologous end joining (NHEJ) in cell. Taken together, our study reveals that in addition to ATP, Ligase IV may use NAD+ as an alternative adenylation donor for NHEJ repair and maintaining genomic stability.
Collapse
Affiliation(s)
- Shih-Hsun Chen
- Department of Cancer Genetics & Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Xiaochun Yu
- Department of Cancer Genetics & Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| |
Collapse
|
5
|
Okafor CD, Lanier KA, Petrov AS, Athavale SS, Bowman JC, Hud NV, Williams LD. Iron mediates catalysis of nucleic acid processing enzymes: support for Fe(II) as a cofactor before the great oxidation event. Nucleic Acids Res 2017; 45:3634-3642. [PMID: 28334877 PMCID: PMC5397171 DOI: 10.1093/nar/gkx171] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 03/08/2017] [Indexed: 12/19/2022] Open
Abstract
Life originated in an anoxic, Fe2+-rich environment. We hypothesize that on early Earth, Fe2+ was a ubiquitous cofactor for nucleic acids, with roles in RNA folding and catalysis as well as in processing of nucleic acids by protein enzymes. In this model, Mg2+ replaced Fe2+ as the primary cofactor for nucleic acids in parallel with known metal substitutions of metalloproteins, driven by the Great Oxidation Event. To test predictions of this model, we assay the ability of nucleic acid processing enzymes, including a DNA polymerase, an RNA polymerase and a DNA ligase, to use Fe2+ in place of Mg2+ as a cofactor during catalysis. Results show that Fe2+ can indeed substitute for Mg2+ in catalytic function of these enzymes. Additionally, we use calculations to unravel differences in energetics, structures and reactivities of relevant Mg2+ and Fe2+ complexes. Computation explains why Fe2+ can be a more potent cofactor than Mg2+ in a variety of folding and catalytic functions. We propose that the rise of O2 on Earth drove a Fe2+ to Mg2+ substitution in proteins and nucleic acids, a hypothesis consistent with a general model in which some modern biochemical systems retain latent abilities to revert to primordial Fe2+-based states when exposed to pre-GOE conditions.
Collapse
Affiliation(s)
- C Denise Okafor
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332 0400, USA
| | - Kathryn A Lanier
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332 0400, USA
| | - Anton S Petrov
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332 0400, USA
| | - Shreyas S Athavale
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332 0400, USA
| | - Jessica C Bowman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332 0400, USA
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332 0400, USA
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332 0400, USA
| |
Collapse
|
6
|
Golyshina OV, Tran H, Reva ON, Lemak S, Yakunin AF, Goesmann A, Nechitaylo TY, LaCono V, Smedile F, Slesarev A, Rojo D, Barbas C, Ferrer M, Yakimov MM, Golyshin PN. Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum Y T. Sci Rep 2017; 7:3682. [PMID: 28623373 PMCID: PMC5473848 DOI: 10.1038/s41598-017-03904-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 05/02/2017] [Indexed: 12/19/2022] Open
Abstract
Ferroplasmaceae represent ubiquitous iron-oxidising extreme acidophiles with a number of unique physiological traits. In a genome-based study of Ferroplasma acidiphilum YT, the only species of the genus Ferroplasma with a validly published name, we assessed its central metabolism and genome stability during a long-term cultivation experiment. Consistently with physiology, the genome analysis points to F. acidiphilum YT having an obligate peptidolytic oligotrophic lifestyle alongside with anaplerotic carbon assimilation. This narrow trophic specialisation abridges the sugar uptake, although all genes for glycolysis and gluconeogenesis, including bifunctional unidirectional fructose 1,6-bisphosphate aldolase/phosphatase, have been identified. Pyruvate and 2-oxoglutarate dehydrogenases are substituted by 'ancient' CoA-dependent pyruvate and alpha-ketoglutarate ferredoxin oxidoreductases. In the lab culture, after ~550 generations, the strain exhibited the mutation rate of ≥1.3 × 10-8 single nucleotide substitutions per site per generation, which is among the highest values recorded for unicellular organisms. All but one base substitutions were G:C to A:T, their distribution between coding and non-coding regions and synonymous-to-non-synonymous mutation ratios suggest the neutral drift being a prevalent mode in genome evolution in the lab culture. Mutations in nature seem to occur with lower frequencies, as suggested by a remarkable genomic conservation in F. acidiphilum YT variants from geographically distant populations.
Collapse
Affiliation(s)
- Olga V Golyshina
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, Gwynedd, UK.
| | - Hai Tran
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, Gwynedd, UK
| | - Oleg N Reva
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, University of Pretoria, Pretoria, 0002, South Africa
| | - Sofia Lemak
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S3E5, Toronto, Ontario, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S3E5, Toronto, Ontario, Canada
| | - Alexander Goesmann
- CeBiTec Bielefeld University, Universitätsstraße 25, D-33615, Bielefeld, Germany
- Department of Bioinformatics and Systems Biology, Justus Liebig Universität Gießen, Heinrich-Buff-Ring 58, D-35392, Gießen, Germany
| | - Taras Y Nechitaylo
- Insect Symbiosis Group, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745, Jena, Germany
| | - Violetta LaCono
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
| | - Francesco Smedile
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
| | - Alexei Slesarev
- Fidelity Systems, Zylacta Corporation, 7965 Cessna Avenue, Gaithersburg, MD, 20879, USA
| | - David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | - Manuel Ferrer
- Institute of Catalysis CSIC, Campus Cantoblanco, 28049, Madrid, Spain
| | - Michail M Yakimov
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
- Immanuel Kant Baltic Federal University, Universitetskaya 1, 36040, Kaliningrad, Russia
| | - Peter N Golyshin
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, Gwynedd, UK
| |
Collapse
|
7
|
Archaeal Nucleic Acid Ligases and Their Potential in Biotechnology. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2015; 2015:170571. [PMID: 26494982 PMCID: PMC4606414 DOI: 10.1155/2015/170571] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/18/2015] [Indexed: 12/23/2022]
Abstract
With their ability to catalyse the formation of phosphodiester linkages, DNA ligases and RNA ligases are essential tools for many protocols in molecular biology and biotechnology. Currently, the nucleic acid ligases from bacteriophage T4 are used extensively in these protocols. In this review, we argue that the nucleic acid ligases from Archaea represent a largely untapped pool of enzymes with diverse and potentially favourable properties for new and emerging biotechnological applications. We summarise the current state of knowledge on archaeal DNA and RNA ligases, which makes apparent the relative scarcity of information on in vitro activities that are of most relevance to biotechnologists (such as the ability to join blunt- or cohesive-ended, double-stranded DNA fragments). We highlight the existing biotechnological applications of archaeal DNA ligases and RNA ligases. Finally, we draw attention to recent experiments in which protein engineering was used to modify the activities of the DNA ligase from Pyrococcus furiosus and the RNA ligase from Methanothermobacter thermautotrophicus, thus demonstrating the potential for further work in this area.
Collapse
|
8
|
Méndez-García C, Peláez AI, Mesa V, Sánchez J, Golyshina OV, Ferrer M. Microbial diversity and metabolic networks in acid mine drainage habitats. Front Microbiol 2015; 6:475. [PMID: 26074887 PMCID: PMC4448039 DOI: 10.3389/fmicb.2015.00475] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 04/29/2015] [Indexed: 11/13/2022] Open
Abstract
Acid mine drainage (AMD) emplacements are low-complexity natural systems. Low-pH conditions appear to be the main factor underlying the limited diversity of the microbial populations thriving in these environments, although temperature, ionic composition, total organic carbon, and dissolved oxygen are also considered to significantly influence their microbial life. This natural reduction in diversity driven by extreme conditions was reflected in several studies on the microbial populations inhabiting the various micro-environments present in such ecosystems. Early studies based on the physiology of the autochthonous microbiota and the growing success of omics-based methodologies have enabled a better understanding of microbial ecology and function in low-pH mine outflows; however, complementary omics-derived data should be included to completely describe their microbial ecology. Furthermore, recent updates on the distribution of eukaryotes and archaea recovered through sterile filtering (herein referred to as filterable fraction) in these environments demand their inclusion in the microbial characterization of AMD systems. In this review, we present a complete overview of the bacterial, archaeal (including filterable fraction), and eukaryotic diversity in these ecosystems, and include a thorough depiction of the metabolism and element cycling in AMD habitats. We also review different metabolic network structures at the organismal level, which is necessary to disentangle the role of each member of the AMD communities described thus far.
Collapse
Affiliation(s)
| | - Ana I. Peláez
- Department of Functional Biology-IUBA, Universidad de OviedoOviedo, Spain
| | - Victoria Mesa
- Department of Functional Biology-IUBA, Universidad de OviedoOviedo, Spain
| | - Jesús Sánchez
- Department of Functional Biology-IUBA, Universidad de OviedoOviedo, Spain
| | | | - Manuel Ferrer
- Department of Applied Biocatalysis, Consejo Superior de Investigaciones Científicas, Institute of CatalysisMadrid, Spain
| |
Collapse
|
9
|
Rodriguez F, Lillington J, Johnson S, Timmel CR, Lea SM, Berks BC. Crystal structure of the Bacillus subtilis phosphodiesterase PhoD reveals an iron and calcium-containing active site. J Biol Chem 2014; 289:30889-99. [PMID: 25217636 PMCID: PMC4223295 DOI: 10.1074/jbc.m114.604892] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The PhoD family of extra-cytoplasmic phosphodiesterases are among the most commonly occurring bacterial phosphatases. The exemplars for this family are the PhoD protein of Bacillus subtilis and the phospholipase D of Streptomyces chromofuscus. We present the crystal structure of B. subtilis PhoD. PhoD is most closely related to purple acid phosphatases (PAPs) with both types of enzyme containing a tyrosinate-ligated Fe3+ ion. However, the PhoD active site diverges from that found in PAPs and uses two Ca2+ ions instead of the single extra Fe2+, Mn2+, or Zn2+ ion present in PAPs. The PhoD crystals contain a phosphate molecule that coordinates all three active site metal ions and that is proposed to represent a product complex. A C-terminal helix lies over the active site and controls access to the catalytic center. The structure of PhoD defines a new phosphatase active site architecture based on Fe3+ and Ca2+ ions.
Collapse
Affiliation(s)
- Fernanda Rodriguez
- From the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU
| | - James Lillington
- the Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, and the Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Steven Johnson
- the Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, and
| | - Christiane R Timmel
- the Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Susan M Lea
- the Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, and
| | - Ben C Berks
- From the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU,
| |
Collapse
|
10
|
Ohara K, Unno H, Oshima Y, Hosoya M, Fujino N, Hirooka K, Takahashi S, Yamashita S, Kusunoki M, Nakayama T. Structural insights into the low pH adaptation of a unique carboxylesterase from Ferroplasma: altering the pH optima of two carboxylesterases. J Biol Chem 2014; 289:24499-510. [PMID: 25043762 DOI: 10.1074/jbc.m113.521856] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To investigate the mechanism for low pH adaptation by a carboxylesterase, structural and biochemical analyses of EstFa_R (a recombinant, slightly acidophilic carboxylesterase from Ferroplasma acidiphilum) and SshEstI (an alkaliphilic carboxylesterase from Sulfolobus shibatae DSM5389) were performed. Although a previous proteomics study by another group showed that the enzyme purified from F. acidiphilum contained an iron atom, EstFa_R did not bind to iron as analyzed by inductively coupled plasma MS and isothermal titration calorimetry. The crystal structures of EstFa_R and SshEstI were determined at 1.6- and 1.5-Å resolutions, respectively. EstFa_R had a catalytic triad with an extended hydrogen bond network that was not observed in SshEstI. Quadruple mutants of both proteins were created to remove or introduce the extended hydrogen bond network. The mutation on EstFa_R enhanced its catalytic efficiency and gave it an alkaline pH optimum, whereas the mutation on SshEstI resulted in opposite effects (i.e. a decrease in the catalytic efficiency and a downward shift in the optimum pH). Our experimental results suggest that the low pH optimum of EstFa_R activity was a result of the unique extended hydrogen bond network in the catalytic triad and the highly negatively charged surface around the active site. The change in the pH optimum of EstFa_R happened simultaneously with a change in the catalytic efficiency, suggesting that the local flexibility of the active site in EstFa_R could be modified by quadruple mutation. These observations may provide a novel strategy to elucidate the low pH adaptation of serine hydrolases.
Collapse
Affiliation(s)
- Kazuhiro Ohara
- From the Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-11, Sendai 980-8579, Japan
| | - Hideaki Unno
- Graduate School of Engineering, Nagasaki University, Bunkyo-machi 1-14, Nagasaki 852-8521, Japan, and
| | - Yasuhiro Oshima
- From the Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-11, Sendai 980-8579, Japan
| | - Miho Hosoya
- From the Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-11, Sendai 980-8579, Japan
| | - Naoto Fujino
- From the Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-11, Sendai 980-8579, Japan
| | - Kazutake Hirooka
- From the Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-11, Sendai 980-8579, Japan
| | - Seiji Takahashi
- From the Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-11, Sendai 980-8579, Japan
| | - Satoshi Yamashita
- From the Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-11, Sendai 980-8579, Japan,
| | - Masami Kusunoki
- Faculty of Life and Environmental Sciences, University of Yamanashi, 4-3-37 Takeda, Kofu 400-8511, Japan
| | - Toru Nakayama
- From the Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-11, Sendai 980-8579, Japan
| |
Collapse
|
11
|
Shrivastava N, Nag JK, Misra-Bhattacharya S. Molecular characterization of NAD+-dependent DNA ligase from Wolbachia endosymbiont of lymphatic filarial parasite Brugia malayi. PLoS One 2012; 7:e41113. [PMID: 22815933 PMCID: PMC3397958 DOI: 10.1371/journal.pone.0041113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 06/21/2012] [Indexed: 11/19/2022] Open
Abstract
The lymphatic filarial parasite, Brugia malayi contains Wolbachia endobacteria that are essential for development, viability and fertility of the parasite. Therefore, wolbachial proteins have been currently seen as the potential antifilarial drug targets. NAD(+)-dependent DNA ligase is characterized as a promising drug target in several organisms due to its crucial, indispensable role in DNA replication, recombination and DNA repair. We report here the cloning, expression and purification of NAD(+)-dependent DNA ligase of Wolbachia endosymbiont of B. malayi (wBm-LigA) for its molecular characterization. wBm-LigA has all the domains that are present in nearly all the eubacterial NAD(+)-dependent DNA ligases such as N-terminal adenylation domain, OB fold, helix-hairpin-helix (HhH) and BRCT domain except zinc-binding tetracysteine domain. The purified recombinant protein (683-amino acid) was found to be biochemically active and was present in its native form as revealed by the circular dichroism and fluorescence spectra. The purified recombinant enzyme was able to catalyze intramolecular strand joining on a nicked DNA as well as intermolecular joining of the cohesive ends of BstEII restricted lamda DNA in an in vitro assay. The enzyme was localized in the various life-stages of B. malayi parasites by immunoblotting and high enzyme expression was observed in Wolbachia within B. malayi microfilariae and female adult parasites along the hypodermal chords and in the gravid portion as evident by the confocal microscopy. Ours is the first report on this enzyme of Wolbachia and these findings would assist in validating the antifilarial drug target potential of wBm-LigA in future studies.
Collapse
Affiliation(s)
- Nidhi Shrivastava
- Division of Parasitology, Central Drug Research Institute, Lucknow, Uttar Pradesh, India
| | - Jeetendra Kumar Nag
- Division of Parasitology, Central Drug Research Institute, Lucknow, Uttar Pradesh, India
| | | |
Collapse
|
12
|
Ishino Y, Ishino S. Rapid progress of DNA replication studies in Archaea, the third domain of life. SCIENCE CHINA-LIFE SCIENCES 2012; 55:386-403. [PMID: 22645083 DOI: 10.1007/s11427-012-4324-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 04/20/2012] [Indexed: 02/04/2023]
Abstract
Archaea, the third domain of life, are interesting organisms to study from the aspects of molecular and evolutionary biology. Archaeal cells have a unicellular ultrastructure without a nucleus, resembling bacterial cells, but the proteins involved in genetic information processing pathways, including DNA replication, transcription, and translation, share strong similarities with those of Eukaryota. Therefore, archaea provide useful model systems to understand the more complex mechanisms of genetic information processing in eukaryotic cells. Moreover, the hyperthermophilic archaea provide very stable proteins, which are especially useful for the isolation of replisomal multicomplexes, to analyze their structures and functions. This review focuses on the history, current status, and future directions of archaeal DNA replication studies.
Collapse
Affiliation(s)
- Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan.
| | | |
Collapse
|
13
|
White MF, Dillingham MS. Iron-sulphur clusters in nucleic acid processing enzymes. Curr Opin Struct Biol 2011; 22:94-100. [PMID: 22169085 DOI: 10.1016/j.sbi.2011.11.004] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 11/15/2011] [Accepted: 11/16/2011] [Indexed: 12/25/2022]
Abstract
Several unexpected reports of iron-sulphur clusters in nucleic acid binding proteins have recently appeared in the literature. Once thought to be relatively rare in these systems, iron-sulphur clusters are now known to be essential components of diverse nucleic acid processing machinery including glycosylases, primases, helicases, nucleases, transcription factors, RNA polymerases and RNA methyltransferases. In many cases, the function of the cluster is poorly understood and crystal structures of these iron-sulphur enzymes reveal little in common between them. In this article, we review the recent developments in the field and discuss to what extent there might exist common mechanistic roles for iron-sulphur clusters in nucleic acid enzymes.
Collapse
Affiliation(s)
- Malcolm F White
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK.
| | | |
Collapse
|
14
|
Acidophilic bacteria and archaea: acid stable biocatalysts and their potential applications. Extremophiles 2011; 16:1-19. [PMID: 22080280 DOI: 10.1007/s00792-011-0402-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Accepted: 10/05/2011] [Indexed: 01/05/2023]
Abstract
Acidophiles are ecologically and economically important group of microorganisms, which thrive in acidic natural (solfataric fields, sulfuric pools) as well as artificial man-made (areas associated with human activities such as mining of coal and metal ores) environments. They possess networked cellular adaptations to regulate pH inside the cell. Several extracellular enzymes from acidophiles are known to be functional at much lower pH than the cytoplasmic pH. Enzymes like amylases, proteases, ligases, cellulases, xylanases, α-glucosidases, endoglucanases, and esterases stable at low pH are known from various acidophilic microbes. The possibility of improving them by genetic engineering and directed evolution will further boost their industrial applications. Besides biocatalysts, other biomolecules such as plasmids, rusticynin, and maltose-binding protein have also been reported from acidophiles. Some strategies for circumventing the problems encountered in expressing genes encoding proteins from extreme acidophiles have been suggested. The investigations on the analysis of crystal structures of some acidophilic proteins have thrown light on their acid stability. Attempts are being made to use thermoacidophilic microbes for biofuel production from lignocellulosic biomass. The enzymes from acidophiles are mainly used in polymer degradation.
Collapse
|
15
|
Bonnefoy V, Holmes DS. Genomic insights into microbial iron oxidation and iron uptake strategies in extremely acidic environments. Environ Microbiol 2011; 14:1597-611. [DOI: 10.1111/j.1462-2920.2011.02626.x] [Citation(s) in RCA: 144] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
16
|
Environmental, biogeographic, and biochemical patterns of archaea of the family Ferroplasmaceae. Appl Environ Microbiol 2011; 77:5071-8. [PMID: 21685165 DOI: 10.1128/aem.00726-11] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
About 10 years ago, a new family of cell wall-deficient, iron-oxidizing archaea, Ferroplasmaceae, within the large archaeal phylum Euryarchaeota, was described. In this minireview, I summarize the research progress achieved since then and report on the current status of taxonomy, biogeography, physiological diversity, biochemistry, and other research areas involving this exciting group of acidophilic archaea.
Collapse
|
17
|
Watlinga HR, Watkinb ELJ, Ralphe DE. The resilience and versatility of acidophiles that contribute to the bio-assisted extraction of metals from mineral sulphides. ENVIRONMENTAL TECHNOLOGY 2010; 31:915-933. [PMID: 20662381 DOI: 10.1080/09593331003646646] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In this paper, a brief outline is presented on acidic ferric ion oxidation of mineral sulphides for the extraction of metals in both stirred tank reactors for mineral concentrates and heaps for low-grade ores. The identities and capabilities of the relatively few acidophiles that assist the oxidative processes are summarized and their responses to selected extremes in their growth environments described. Individually, the organisms adapt to the presence of high concentrations of heavy metals and other elements in the bioleaching environment, tolerate a wide range of acidities and can recover from prolonged exposure to temperatures significantly above their preferred temperatures for growth. However, the presence of chloride in their acidic environment presents a significant physiological challenge. Species that exhibit a chemotactic response and attachment to sulphide surfaces, where they can create their own micro-environments, would be favoured in both heap bioreactors with low availability of energy substrates and physically aggressive, agitated continuous stirred-tank reactor environments treating concentrates.
Collapse
Affiliation(s)
- H R Watlinga
- Parker Centre for Integrated Hydrometallurgy Solutions: CSIRO Minerals Down Under Flagship, P.O. Box 7229, Karawara, Western Australia 6152, Australia.
| | | | | |
Collapse
|
18
|
Abstract
We are becoming increasingly aware of the role played by archaea in the biogeochemical cycling of the elements. Metabolism of metals is linked to fundamental metabolic functions, including nitrogen fixation, energy production, and cellular processes based on oxidoreductions. Comparative genomic analyses have shown that genes for metabolism, resistance, and detoxification of metals are widespread throughout the archaeal domain. Archaea share with other organisms strategies allowing them to utilize essential metals and maintain metal ions within a physiological range, although comparative proteomics show, in a few cases, preferences for specific genetic traits related to metals. A more in-depth understanding of the physiology of acidophilic archaea might lead to the development of new strategies for the bioremediation of metal-polluted sites and other applications, such as biomining.
Collapse
Affiliation(s)
- Elisabetta Bini
- Department of Biochemistry and Microbiology, Rutgers-The State University of New Jersey, New Brunswick, NJ, USA.
| |
Collapse
|
19
|
Paper and market watch. Biotechnol J 2008. [DOI: 10.1002/biot.200890085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|